Temporal and spatial distribution of physico-chemical and water quality parameters and their correlation with meteorological and hydrological data, was investigated for anoxic lagoons, in Greece. Monthly variations of parameters like temperature, salinity, dissolved oxygen, chlorophyll-a, total phosphorus etc., along the Aitoliko lagoon water column, were recorded and studied at 14 stations. Throughout the sampling period, in lagoon's water column three layers were determined: the surface low density layer (11.49-16.15), the layer with the steep density gradient and the deep dense (19.78-20.62) water below the depth of 20 m. The depth of the surface and pycnocline layers depends on seasonal surface salinity (20.53-22.43 per hundred) and temperature (12.48-28.40 degrees C) alterations. Lagoon's monimolimnion was extended, below the depth of 20 m and had constant temperature and salinity equal to about 13 degrees C and 27 per hundred respectively. Meteorological conditions control temperature (R2=0.845) and dissolved oxygen (R2=0.576) monthly changes, in lagoon's epilimnion, while salinity seems to be related with the salt/fresh water budget into Aitoliko lagoon. Epilimnetic chlorophyll-a (3.29-14.89 microg l(-1)) and total phosphorus (13.33-36.31 microg l(-1)) concentrations classify Aitoliko lagoon as a mesotrophic environment (40<TSI (Chl-a)<55, 40<TSI (TP)<60). The vertical distribution of dissolved oxygen in the water column was always of special interest. During the last decades the Aitoliko lagoon was reported as a permanent anoxic basin. The depth of the anoxic layer gradually decreased and reached 5 m depth during 2003-2004. In the present study, the anoxic layer was limited below the depth of 18 m during summer. The most interesting is the dissolved oxygen presence in lagoon's monimolimnion during January and February, 2007. In this study, for the first time, Aitoliko lagoon was reported as seasonal anoxic basin.